Location: Molecular Plant Pathology Laboratory2015 Annual Report
1. Improve the efficiency of developing alfalfa with greater tolerance to biotic and abiotic stresses by characterizing gene-stress responses and pathways. Biotic and abiotic stresses cause significant yield losses in alfalfa and greatly reduce the crop’s productivity. Understanding the molecular mechanisms of stress tolerance and the ways by which stress-responsive genes are regulated is essential for improvement of alfalfa adaptability and breeding programs. 2. Aid plant breeders in improving alfalfa productivity and adaptability by implementing genetic and genomic approaches to improve traits related to biotic and abiotic stress tolerance, including, but not limited to, root-knot nematodes and salinity tolerance. Data on stress-responsive genes obtained in this study and other information on alfalfa genomics will be used to identify molecular markers associated with resistance and adaptation to abiotic and biotic stresses in alfalfa.
The research project will identify stress-responsive gene-candidates in alfalfa and assign them to cognate functional groups related to specific stress responses. It will quantify and confirm roles of the selected genes in adaptation to abiotic and biotic stresses and in regulation of stress responses. Sequence polymorphism in genes underlying stress tolerance will be delineated and molecular markers associated with resistance and adaptation of alfalfa to biotic and abiotic stresses developed. Markers will be validated through cooperative research collaborations.
Next generation sequencing (NGS) was performed on plant bacterial pathogen, Pseudomonas syringae pv. syringae causing bacterial stem blight disease in alfalfa to estimate bacterial viability under oxidative burst. Expression of bacterial genes is being analyzed. NGS was performed on alfalfa varieties contrasting in resistance to root knot nematode (RKN, Meloidogyne spp) and candidate genes with putative roles in resistance against RKN were identified. NGS was performed on alfalfa varieties contrasting in salt tolerance and candidate genes with putative roles in adaptation to salt stress were identified. Molecular markers (simple sequence repeats, SSRs) are being developed based on the data obtained from RNA sequencing experiments and their polymorphism is being determined in different alfalfa accessions. VIGS (virus-induced gene silencing) vector for alfalfa genomic studies is being developed based on the low pathogenic Alfalfa latent carlavirus. Progress is directly related to the Objective 1 of the Project Plan: Improve the efficiency of developing alfalfa with greater tolerance to biotic and abiotic factors by characterizing gene-stress responses and pathways.
1. Identification of the candidate genes involved in alfalfa resistance to the root knot nematode. Comprehensive gene expression profiling and analysis of transcriptional changes during alfalfa interaction with the economically important root-knot nematode, M. incognita, led to identification of the candidate genes involved in resistance to root knot nematode. The acquired knowledge will serve as a resource for improvement of alfalfa adaptability and breeding programs.
2. Large scale transcriptome profiling of Pseudomonas syringae pv. syringae, the bacterial stem blight pathogen. Alfalfa yield losses from the bacterial stem blight pathogen, Pseudomonas syringae pv. syringae, can be as high as 50% of the first harvest. More information on the physiological and molecular events of host inhibitory environment on the pathogen is needed to develop resistant cultivars. ARS researchers in Beltsville, Maryland, conducted large scale transcriptome profiling of Pseudomonas syringae pv. syringae treated by the major extracellular phenolic compound, acetosyringone, and identified the bacterial genes affected by the treatment. The findings offer insight into what might happen in the plant when bacterial pathogens are first encountered and host defense responses are triggered. The acquired knowledge will improve our understanding of the molecular mechanisms of stress tolerance.
3. Genome sequence and structure of Alfalfa latent virus (ALV). Alfalfa latent virus (ALV) is recognized as a strain of Pea streak virus that affects peas, beans and many other plant species and is known for more than 60 years. ARS researchers in Beltsville, Maryland, completed the first complete nucleotide sequence of the ALV and determined the genome structure of the virus. The overall goal of this project is to develop an efficient virus-induced gene silencing (VIGS) vector that is not currently available for alfalfa genomic studies. This novel methodology will help researchers to gain critical insights for alfalfa breeding programs.
Postnikova, O., Nemchinov, L.G. 2015. Natural antisense transcripts associated with salinity response in alfalfa. The Plant Genome. 8:1-5.
Nemchinov, L.G., Shao, J.Y., Postnikova, O.A. 2015. Complete genome sequence of the alfalfa latent virus. Genome Announcements. 3(2):e00250-15.